Mechanical Pruning Induces Distinct Metabolic Responses in Slender Spindle-Shaped Apple Orchards

Mechanical pruning has emerged as a viable alternative to traditional hand pruning in apple orchards in labor-constrained and aging population workforces. While mechanical pruning reduces labor demand and enhances operational efficiency, their effects on tree physiology and fruit development remain poorly understood. In this study, we examined the physiological and transcriptional responses of apple trees to mechanical pruning (MP) and hand pruning (HP), with a focus on hormone metabolism, photosynthetic activity, and stress adaptation. Pruning treatments were applied in an orchard using a tractor-mounted mechanical pruner and manual shears, and distinct metabolic responses after pruning were assessed over multiple time points using transcriptomic analysis. At 168 h after MP, trees exhibited downregulation of <i>MdLhcb</i> genes, indicating a reduction in light harvesting capacity. In addition, <i>MdDFR</i>, a key gene in flavonoid biosynthesis, was also downregulated, suggesting a suppression of secondary metabolism and a distinct physiological response to MP. In addition, stress-responsive genes such as <i>MdNHL3</i> were rather upregulated, indicating the activation of adaptive signaling networks. Conversely, HP trees showed relatively moderate responses in the same pathways, suggesting pruning method-specific regulatory mechanisms. These findings highlight how pruning methods distinctly influence tree recovery and gene expression dynamics, offering insights into optimizing pruning systems for sustainable and high-quality apple production under labor-constrained conditions.